Design of structure-based reverse transcriptase inhibitors.

Based on the crystallographic structure of the active site in the reverse transcriptase (RT) of human immunodeficiency virus (HIV), a group of hydrophobic polyadenylic acid (5') derivatives were designed and synthesized as inhibitors of the enzyme. These compounds were found to inhibit all six of the RTs tested, with IC50 = 10(-11)-10(-8) M, but did not inhibit either RNA polymerase II (even at 10(-5) M) or DNA polymerase I up to 10(-6) M inhibitor concentration. The underivatized poly(A) did not inhibit any of the RTs tested under the same conditions. In aqueous solutions of purified HIV-1 RT, poly-2'-O-(2,4-dinitrophenyl)-oligo(A) was found to inhibit the enzyme reversibly and compete with the primer-template poly(A)-(dT)12, whereas poly-2'-O-(3-fluoro-4,6-dinitrophenyl)-poly(A) was found to inactivate HIV-1 RT irreversibly by covalent labeling. A comparison of physicochemical properties of the hybrids poly(A)-poly(dT) and dinitrophenyl-poly(A)-poly(dT) shows that the hydrophobic dinitrophenyl groups stabilize double helical structures. These inhibitors were also found to be effective in keeping susceptible lymphocytes viable in the presence of HIV-1 (wild type). The effective inhibitor concentrations (EC50) were found to be 0.2-2.6 microgram/ml. No toxic effect on the host cells was found even at 100-1000-fold higher inhibitor concentrations.